# To put any missing (heavy) atoms on the model and to reorder the atoms 
# according to the MODELLER/CHARMM order:
#
# Input : MODEL; filename of the input atom file
# Output: complete model in memory 
#

SUBROUTINE ROUTINE = 'complete'

# Use this to put on heavy atoms only:
READ_TOPOLOGY FILE = '${LIB}/top_heav.lib'

# Use this to put on all atoms, including hydrogens:
# READ_TOPOLOGY FILE = '${LIB}/top.lib'

READ_PARAMETERS FILE = '${LIB}/par.lib'

# read the sequence from the input atom file:
READ_MODEL FILE = MODEL

# generate the internal coordinates
GENERATE_TOPOLOGY
CALL ROUTINE = 'special_patches'

# copy the known atom coordinates from MODEL to model in the memory
DELETE_ALIGNMENT
SEQUENCE_TO_ALI ATOM_FILES = MODEL, ALIGN_CODES = MODEL
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES MODEL, ;
                ALIGN_CODES = ALIGN_CODES MODEL
TRANSFER_XYZ

# Fill in the coordinates for the missing atoms:
BUILD_MODEL INITIALIZE_XYZ = 'OFF'

RETURN
END_SUBROUTINE